Congratulations!
The DIS is a great place to start planning, though you may also want to pick up a guidebook for an overview before you dive into the specific questions and answers found all over these boards.
I think a case can be made for just about any Disney hotel as being great for a honeymoonit really depends on what you are after. Do you want to be near the parks? Which parks? Do you plan to use many of the amenities at the resorts or mostly be in the parks all day? Will you have a car? Is there a particular decor or theme that appeals to you? etc....
The Contemporary is great because it's so close to the Magic Kingdom and all the restaurants and fireworks-viewing spots of the other hotels on the monorail line. The Grand Floridian's Victorian theme and exceptional customer service make it appealing to lots of honeymooners, while others prefer the tropical feel of the Polynesian. I like the BoardWalk-area resorts because I spend the most time at Epcot and I like their decor. There are SO many factors to consider that are unique to your taste and situation.
As for booking, I usually start with a reservation as soon as I know I'm going and then keep my eyes peeled for discounts and promotions that come out along the way. You can then modify or rebook as needed, but at least you had something to start with. (This is all for room-only reservationspackages have rules that might make this trickier.)